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Table 2 Selected differentially expressed genes closely related to cell wall biosynthesis and C1 pathways from 6-week-old stems of fpgs1, ccoaomt1, and fpgs1ccoaomt1 plants

From: Combining loss of function of FOLYLPOLYGLUTAMATE SYNTHETASE1 and CAFFEOYL-COA 3-O-METHYLTRANSFERASE1 for lignin reduction and improved saccharification efficiency in Arabidopsis thaliana

AGI Gene name/putative function fpgsl/WT ccoaomt1/WT fpgs1ccoaomt1/WT fpgs1ccoaomt1/fpgs1 fpgs1ccoaomt1/ccoaomt1
Fold change P-value Fold change P-value Fold change P-value Fold change P-value Fold change P-value
 At5g05980 FOLYLPOLYGLUTAMATE SYNTHETASE 1 (FPGS1) 0.08 0 1.12 0.1 0.09 0 1.10 0.7 0.08 0
 At4g34050 CAFFEOYL COENZYME A O-METHYLTRANSFERASE 1 (CCoA0MT1) 1.01 0.95 0.04 0 0.06 0 0.06 0 1.58 0.02
Phenylpropanoid/lignin biosynthesis
 At2g44130 KELCH REPEAT F-B0X 39 (KFB39): phenylpropanoid metabolic process 0.42 1.4E−138 0.12 0 0.11 0 0.27 0.00 0.90 0.29
 At3g59940 KELCH REPEAT F-BOX 5O (KFB50): phenylpropanoid metabolic process 0.64 0 0.47 0 0.44 0 0.69 1.88E−04 0.93 0.52
 At1g80440 KELCH REPEAT F-BOX 20 (KPB20): phenylpropanoid metabolic process 1.04 0.09 0.47 0 0.60 0 0.58 1.17E−05 1.29 0.15
 At3g53260 PHENYLALANINE LYASE 2 (PAL2): 1.26 4.82E−14 1.83 1.1E−14 1.73 2.3E−08 1.37 1.4E−40 0.94 0.34
 At1g80820 CINNAMOYL COA REDUCTASE (AtCCR2) 2.82 0 7.18 0 8.56 0 3.04 4.58E−45 1.19 0.23
 At1g20510 4CL-LIKE1: OPC-8:0 COA LIGASE1 (0PCLI) 2.43 0 2.55 0 2.57 0 1.06 0.60 1.01 0.93
 At2g29130 LACCASE 2 (AtLAC2) 0.37 0 1.33 6.04E−07 1.26 8.61E−05 3.45 2.25E−102 0.95 0.83
 At2g37130 PEROXIDASE 21 (AtPrx21) 1.27 3.94E−04 0.44 4.16E−33 0.34 0 0.27 2.25E−13 0.77 0.03
 At4g38620 AtMYB4: regulation of phenylpropanoid metabolic process 0.60 0 0.37 0 0.51 0 0.86 1.26E−05 1.37 1.02E−12
Cell well synthesis
 At3g28180 CELLULOSE-SYNTHASE LIKE C4 (AtCSLC4) 2.18 0 4.24 0 4.22 0 1.93 2.81E−10 1.00 0.98
 At5g57560 CELL WALL-MODIFYING ENZYME, XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 22 (AtXTH22) 7.37 0 19.68 0 17.02 0 2.31 3.24E−98 0.86 0.12
 At3g16720 RING-H2 PROTEIN, TOXICOS EN LEVADURA 2 3.54 0 3.28 0 5.89 0 1.66 7.46E−22 1.79 6.18E−05
 At3g45960 EXPANSIN-LIKE A3 (EXPL3) 6.25 0 14.99 0 14.91 0 2.38 2.90E−12 0.99 0.87
 At3g45970 EXPANSIN-LIKE A1 (EXPL1) 4.17 8.27E−102 14.41 0 9.51 0 2.28 2.38E−07 0.66 0.03
 At4g38400 EXPANSIN-LIKE A2 (EXLA2) 1.31 1.56E−03 2.17 1.41E−33 2.37 9.2E−46 1.82 5.93E−04 1.09 0.38
Glucosinolates metabolism
 At4g03050 AOP3: involved in glucosinolate biosynthesis 1.08 0.54 1.07 0.01 0.31 1.19E−07 0.28 1.27E−07 0.29 0
 At1g21120 COMT-LIKE GENE: INDOLE GLUCOSINOLATE METHYLTRANSFERASE 2 (IGMT2) 1.69 0 4.70 0 4.18 0 2.47 0 0.89 0.15
 At1g21110 COMT-LIKE GENE: INDOLE GLUCOSINOLATE METHYLTRANSFERASE 3 (1GMT3) 2.83 0 3.65 3.40E−127 10.33 0 3.65 0 2.83 0
 At1g21130 COMT-LIKE GENE: INDOLE GLUCOSINOLATE METHYLTRANSFERASE 4 (IGMT4) 2.20 4.31E−06 1.69 0.009 2.93 1.32E−13 2.33 0.010 1.74 1.13E−05
One carbon metabolism
 At3g22740 HOMOCYSTEINE S-METHYLTRANSFERASE (HMT3) 1.59 5.29E−102 1.50 0 0.53 0 033 1.66E−29 0.35 0
  1. P-values were obtained by associative analysis [81]. The italic highlighted genes were significant, with ratio of a 1.5 times and P < 2.20E−06 (a Bonferroni-corrected P-value cutoff)